Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:41 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 709/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
fgsea 1.28.0 (landing page) Alexey Sergushichev
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the fgsea package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fgsea.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: fgsea |
Version: 1.28.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings fgsea_1.28.0.tar.gz |
StartedAt: 2023-11-02 10:30:18 -0000 (Thu, 02 Nov 2023) |
EndedAt: 2023-11-02 10:34:32 -0000 (Thu, 02 Nov 2023) |
EllapsedTime: 254.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: fgsea.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings fgsea_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/fgsea.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘fgsea/DESCRIPTION’ ... OK * this is package ‘fgsea’ version ‘1.28.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘fgsea’ can be installed ... OK * used C++ compiler: ‘g++ (GCC) 10.3.1’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 10.3Mb sub-directories of 1Mb or more: data 1.1Mb extdata 3.9Mb libs 5.0Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE setUpBPPARAM: warning in MulticoreParam(workers = nproc, progress = TRUE): partial argument match of 'progress' to 'progressbar' addGesecaScores: no visible global function definition for ‘DefaultAssay’ addGesecaScores: no visible global function definition for ‘GetAssay’ collapsePathways: no visible binding for global variable ‘pathway’ collapsePathways: no visible binding for global variable ‘ES’ collapsePathwaysGeseca: no visible binding for global variable ‘pvalCond’ collapsePathwaysGeseca: no visible binding for global variable ‘pathway’ collapsePathwaysGeseca: no visible binding for global variable ‘reciprocalPvalCond’ collapsePathwaysGeseca: no visible binding for global variable ‘pScore’ collapsePathwaysGeseca: no visible binding for global variable ‘pval’ fgseaMultilevel: no visible binding for global variable ‘modeFraction’ fgseaMultilevel: no visible binding for global variable ‘denomProb’ fora: no visible binding for global variable ‘pval’ geseca: no visible binding for global variable ‘gsScore’ geseca: no visible binding for global variable ‘log2err’ geseca: no visible binding for global variable ‘nGeScore’ geseca: no visible binding for global variable ‘pctVar’ geseca: no visible binding for global variable ‘size’ geseca: no visible binding for global variable ‘pathway’ geseca: no visible global function definition for ‘.’ geseca: no visible binding for global variable ‘pval’ geseca: no visible binding for global variable ‘padj’ gesecaSimple: no visible binding for global variable ‘pctVar’ gesecaSimple: no visible binding for global variable ‘size’ gesecaSimple: no visible binding for global variable ‘pval’ gesecaSimpleImpl: no visible binding for global variable ‘pval’ gesecaSimpleImpl: no visible binding for global variable ‘nGeScore’ gesecaSimpleImpl: no visible binding for global variable ‘padj’ gesecaSimpleImpl: no visible binding for global variable ‘size’ plotCoregulationProfile: no visible binding for global variable ‘id’ plotCoregulationProfile: no visible binding for global variable ‘gene’ plotCoregulationProfile: no visible binding for global variable ‘expressionValue’ plotCoregulationProfile: no visible binding for global variable ‘x’ plotCoregulationProfile: no visible binding for global variable ‘y’ plotCoregulationProfile: no visible binding for global variable ‘condition’ plotCoregulationProfileReduction: no visible global function definition for ‘DefaultAssay’ plotCoregulationProfileSpatial: no visible global function definition for ‘DefaultAssay’ plotGesecaTable: no visible global function definition for ‘modifyList’ plotGesecaTable: no visible binding for global variable ‘pathway’ plotGesecaTable: no visible binding for global variable ‘value’ plotGesecaTable : <anonymous>: no visible binding for global variable ‘pathway’ plotGesecaTable : <anonymous>: no visible binding for global variable ‘value’ plotGseaTable: no visible global function definition for ‘modifyList’ Undefined global functions or variables: . DefaultAssay ES GetAssay condition denomProb expressionValue gene gsScore id log2err modeFraction modifyList nGeScore pScore padj pathway pctVar pval pvalCond reciprocalPvalCond size value x y Consider adding importFrom("utils", "modifyList") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotGseaTable 17.986 2.774 17.876 collapsePathways 12.052 0.667 9.185 mapIdsList 9.331 0.685 7.837 fgseaSimple 6.644 1.051 3.264 fgsea 7.077 0.367 3.970 fgseaMultilevel 6.764 0.415 3.615 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/fgsea.Rcheck/00check.log’ for details.
fgsea.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL fgsea ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘fgsea’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ScoreCalculation.cpp -o ScoreCalculation.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ScoreRuler.cpp -o ScoreRuler.o In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/constants/constants.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:20, from util.h:5, from ScoreRuler.cpp:2: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ ScoreRuler.cpp: In member function ‘void ScoreRuler::extend(double, int, double)’: ScoreRuler.cpp:76:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 76 | for (moves = 0; moves < sampleSize * genesetSize;) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c esCalculation.cpp -o esCalculation.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c fastGSEA.cpp -o fastGSEA.o In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/constants/constants.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:20, from util.h:5, from fastGSEA.cpp:13: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ fastGSEA.cpp: In function ‘Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)’: fastGSEA.cpp:446:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 446 | for (int j = 0; j < S.size(); ++j) { | ~~^~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c fgseaMultilevel.cpp -o fgseaMultilevel.o fgseaMultilevel.cpp: In function ‘Rcpp::DataFrame fgseaMultilevelCpp(const NumericVector&, const NumericVector&, int, int, int, double, bool)’: fgseaMultilevel.cpp:10:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 10 | for (int i = 0; i < posRanks.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/constants/constants.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:20, from util.h:5, from fgseaMultilevelSupplement.cpp:3: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ fgseaMultilevelSupplement.cpp: In member function ‘void EsRuler::duplicateSamples()’: fgseaMultilevelSupplement.cpp:40:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 40 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) { | ~~~~~~~~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:50:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 50 | for (int sampleId = 0; 2 * sampleId < sampleSize; sampleId++) { | ~~~~~~~~~~~~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:59:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 59 | for (int sampleId = 0; 2 * sampleId < sampleSize - 2; sampleId++) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ fgseaMultilevelSupplement.cpp: In member function ‘void EsRuler::extend(double, int, double)’: fgseaMultilevelSupplement.cpp:73:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 73 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) { | ~~~~~~~~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:77:16: warning: unused variable ‘currentES’ [-Wunused-variable] 77 | double currentES = calcES(ranks, currentSamples[sampleId]); | ^~~~~~~~~ fgseaMultilevelSupplement.cpp:90:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 90 | for (int j = 0; j < sampleSize; ++j) { | ~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:97:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 97 | for (int i = 0; i < sampleSize; ++i) { | ~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:112:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 112 | for (int moves = 0; moves < sampleSize * pathwaySize;) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:113:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 113 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) { | ~~~~~~~~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:118:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 118 | for (int i = 0; i < sampleSize; ++i) { | ~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp: In member function ‘int EsRuler::perturbate(const std::vector<double>&, int, EsRuler::SampleChunks&, double, std::mt19937&)’: fgseaMultilevelSupplement.cpp:260:14: warning: unused variable ‘fl’ [-Wunused-variable] 260 | bool fl = false; | ^~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c geseca.cpp -o geseca.o geseca.cpp: In function ‘Rcpp::List gesecaCpp(const NumericMatrix&, const NumericVector&, unsigned int, unsigned int, int, double)’: geseca.cpp:9:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 9 | for (unsigned i = 0; i < E.nrow(); i++){ | ~~^~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c util.cpp -o util.o In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/constants/constants.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:20, from util.h:5, from util.cpp:1: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o fgsea.so RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-fgsea/00new/fgsea/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fgsea)
fgsea.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # setting R_TESTS to empty string because of > # https://github.com/hadley/testthat/issues/144 > # revert this when that issue in R is fixed. > Sys.setenv("R_TESTS" = "") > > library(testthat) > library(fgsea) > > test_check("fgsea") | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |= | 1% | |== | 3% | |=== | 4% | |==== | 5% | |===== | 7% | |====== | 8% | |======= | 10% | |======== | 11% | |========= | 12% | |========== | 14% | |=========== | 15% | |============ | 16% | |============ | 18% | |============= | 19% | 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═══════════════════════════════════════════════════════════ • On Bioconductor (1): 'test_gsea_analysis.R:80:5' [ FAIL 0 | WARN 1 | SKIP 1 | PASS 128 ] > > proc.time() user system elapsed 122.174 22.808 108.895
fgsea.Rcheck/fgsea-Ex.timings
name | user | system | elapsed | |
calcGseaStat | 0.034 | 0.008 | 0.043 | |
collapsePathways | 12.052 | 0.667 | 9.185 | |
collapsePathwaysORA | 0.170 | 0.008 | 0.176 | |
fgsea | 7.077 | 0.367 | 3.970 | |
fgseaLabel | 0 | 0 | 0 | |
fgseaMultilevel | 6.764 | 0.415 | 3.615 | |
fgseaSimple | 6.644 | 1.051 | 3.264 | |
fora | 1.055 | 0.250 | 0.175 | |
geseca | 3.522 | 0.495 | 3.482 | |
gesecaSimple | 2.000 | 0.143 | 1.537 | |
gmtPathways | 1.267 | 0.216 | 0.097 | |
mapIdsList | 9.331 | 0.685 | 7.837 | |
multilevelError | 0 | 0 | 0 | |
plotEnrichment | 0.002 | 0.000 | 0.002 | |
plotEnrichmentData | 0.583 | 0.035 | 0.629 | |
plotGseaTable | 17.986 | 2.774 | 17.876 | |
reactomePathways | 2.182 | 0.089 | 2.404 | |
writeGmtPathways | 0.043 | 0.000 | 0.043 | |